[2024-01-24 14:14:19,424] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:19,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:19,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg011d9dbe-a4f3-4a9e-a5b5-ec5298b0b730/dqc_reference
[2024-01-24 14:14:20,757] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:20,758] [INFO] Task started: Prodigal
[2024-01-24 14:14:20,759] [INFO] Running command: gunzip -c /var/lib/cwl/stgf820749d-ad01-4439-9430-448b10760a6b/GCF_900460715.1_36725_G02_genomic.fna.gz | prodigal -d GCF_900460715.1_36725_G02_genomic.fna/cds.fna -a GCF_900460715.1_36725_G02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:31,608] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:31,609] [INFO] Task started: HMMsearch
[2024-01-24 14:14:31,609] [INFO] Running command: hmmsearch --tblout GCF_900460715.1_36725_G02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg011d9dbe-a4f3-4a9e-a5b5-ec5298b0b730/dqc_reference/reference_markers.hmm GCF_900460715.1_36725_G02_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:31,928] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:31,930] [INFO] Found 6/6 markers.
[2024-01-24 14:14:31,974] [INFO] Query marker FASTA was written to GCF_900460715.1_36725_G02_genomic.fna/markers.fasta
[2024-01-24 14:14:31,974] [INFO] Task started: Blastn
[2024-01-24 14:14:31,974] [INFO] Running command: blastn -query GCF_900460715.1_36725_G02_genomic.fna/markers.fasta -db /var/lib/cwl/stg011d9dbe-a4f3-4a9e-a5b5-ec5298b0b730/dqc_reference/reference_markers.fasta -out GCF_900460715.1_36725_G02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:32,909] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:32,916] [INFO] Selected 15 target genomes.
[2024-01-24 14:14:32,916] [INFO] Target genome list was writen to GCF_900460715.1_36725_G02_genomic.fna/target_genomes.txt
[2024-01-24 14:14:32,926] [INFO] Task started: fastANI
[2024-01-24 14:14:32,926] [INFO] Running command: fastANI --query /var/lib/cwl/stgf820749d-ad01-4439-9430-448b10760a6b/GCF_900460715.1_36725_G02_genomic.fna.gz --refList GCF_900460715.1_36725_G02_genomic.fna/target_genomes.txt --output GCF_900460715.1_36725_G02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:47,142] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:47,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg011d9dbe-a4f3-4a9e-a5b5-ec5298b0b730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:47,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg011d9dbe-a4f3-4a9e-a5b5-ec5298b0b730/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:47,155] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:14:47,155] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:47,155] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Yersinia ruckeri	strain=NCTC12986	GCA_900460715.1	29486	29486	type	True	100.0	1274	1278	95	conclusive
Yersinia ruckeri	strain=ATCC 29473	GCA_000754815.1	29486	29486	type	True	99.9788	1252	1278	95	conclusive
Yersinia ruckeri	strain=ATCC 29473	GCA_000173755.1	29486	29486	type	True	99.9286	1186	1278	95	conclusive
Yersinia entomophaga	strain=MH96	GCA_001656035.1	935293	935293	type	True	84.144	878	1278	95	below_threshold
Yersinia intermedia	strain=NCTC11469	GCA_900635455.1	631	631	type	True	81.5407	634	1278	95	below_threshold
Yersinia hibernica	strain=CFS1934	GCA_004124235.1	2339259	2339259	type	True	81.1586	611	1278	95	below_threshold
Yersinia aldovae	strain=IP06005	GCA_001091225.1	29483	29483	type	True	81.1376	631	1278	95	below_threshold
Yersinia pseudotuberculosis	strain=NCTC10275	GCA_900637475.1	633	633	suspected-type	True	81.0726	585	1278	95	below_threshold
Yersinia similis	strain=Y228	GCA_001053095.1	367190	367190	type	True	80.9652	587	1278	95	below_threshold
Yersinia mollaretii	strain=ATCC 43969	GCA_013282725.1	33060	33060	type	True	80.9648	644	1278	95	below_threshold
Yersinia kristensenii	strain=ATCC 33638	GCA_000173715.1	28152	28152	type	True	80.8973	588	1278	95	below_threshold
Serratia entomophila	strain=A1	GCA_021462285.1	42906	42906	type	True	79.6397	404	1278	95	below_threshold
Serratia nevei	strain=S15	GCA_008364245.1	2703794	2703794	type	True	79.1226	383	1278	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	78.945	391	1278	95	below_threshold
Rahnella ecdela	strain=FRB 231	GCA_019049625.1	2816250	2816250	type	True	78.8114	362	1278	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:47,157] [INFO] DFAST Taxonomy check result was written to GCF_900460715.1_36725_G02_genomic.fna/tc_result.tsv
[2024-01-24 14:14:47,157] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:47,158] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:47,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg011d9dbe-a4f3-4a9e-a5b5-ec5298b0b730/dqc_reference/checkm_data
[2024-01-24 14:14:47,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:47,197] [INFO] Task started: CheckM
[2024-01-24 14:14:47,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460715.1_36725_G02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460715.1_36725_G02_genomic.fna/checkm_input GCF_900460715.1_36725_G02_genomic.fna/checkm_result
[2024-01-24 14:15:21,961] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:21,962] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:21,978] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:21,978] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:21,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460715.1_36725_G02_genomic.fna/markers.fasta)
[2024-01-24 14:15:21,979] [INFO] Task started: Blastn
[2024-01-24 14:15:21,979] [INFO] Running command: blastn -query GCF_900460715.1_36725_G02_genomic.fna/markers.fasta -db /var/lib/cwl/stg011d9dbe-a4f3-4a9e-a5b5-ec5298b0b730/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460715.1_36725_G02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:23,265] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:23,268] [INFO] Selected 16 target genomes.
[2024-01-24 14:15:23,268] [INFO] Target genome list was writen to GCF_900460715.1_36725_G02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:23,281] [INFO] Task started: fastANI
[2024-01-24 14:15:23,281] [INFO] Running command: fastANI --query /var/lib/cwl/stgf820749d-ad01-4439-9430-448b10760a6b/GCF_900460715.1_36725_G02_genomic.fna.gz --refList GCF_900460715.1_36725_G02_genomic.fna/target_genomes_gtdb.txt --output GCF_900460715.1_36725_G02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:37,531] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:37,544] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:37,544] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000754815.1	s__Yersinia ruckeri	99.9788	1252	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.70	97.63	0.94	0.91	69	conclusive
GCF_001656035.1	s__Yersinia entomophaga	84.149	875	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.84	99.69	0.97	0.94	3	-
GCF_001112925.1	s__Yersinia nurmii	83.9159	839	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900635455.1	s__Yersinia intermedia	81.5383	635	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.02	97.82	0.92	0.88	29	-
GCF_003600645.1	s__Yersinia rochesterensis	81.4374	621	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.46	98.81	0.94	0.91	13	-
GCF_002082245.2	s__Yersinia enterocolitica_E	81.4134	649	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282745.1	s__Yersinia bercovieri	81.2898	626	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.12	95.38	0.94	0.87	18	-
GCF_900460525.1	s__Yersinia kristensenii	81.247	604	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.20	97.89	0.92	0.89	22	-
GCF_901472495.1	s__Yersinia enterocolitica	81.2073	648	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	97.11	96.22	0.89	0.83	185	-
GCF_004124235.1	s__Yersinia hibernica	81.1623	615	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.98	98.46	0.91	0.87	4	-
GCF_001098625.1	s__Yersinia frederiksenii_C	81.1312	646	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	98.63	97.69	0.93	0.89	21	-
GCF_902726525.1	s__Yersinia enterocolitica_H	81.0645	628	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.97	99.97	0.99	0.99	3	-
GCF_001995075.1	s__Yersinia enterocolitica_F	80.9856	646	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.25	99.14	0.94	0.92	3	-
GCF_001053095.1	s__Yersinia similis	80.954	588	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.47	99.21	0.94	0.92	9	-
GCF_013282725.1	s__Yersinia mollaretii	80.921	645	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	96.95	95.82	0.92	0.88	25	-
GCF_900460465.1	s__Yersinia pestis	80.9113	578	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Yersinia	95.0	99.78	97.10	0.96	0.85	655	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:37,546] [INFO] GTDB search result was written to GCF_900460715.1_36725_G02_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:37,546] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:37,550] [INFO] DFAST_QC result json was written to GCF_900460715.1_36725_G02_genomic.fna/dqc_result.json
[2024-01-24 14:15:37,550] [INFO] DFAST_QC completed!
[2024-01-24 14:15:37,551] [INFO] Total running time: 0h1m18s